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Modified Nucleobases

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Photoinduced Phenomena in Nucleic Acids I

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 355))

Abstract

Various molecules which are similar to the natural nucleobases exist in nature or have been synthetically developed. In this chapter we review work on the photophysical properties of several modified nucleobases, focusing particularly on how these properties differ from those of the natural nucleobases. We discuss studies that give physical insight into how the molecular structure can be related to photophysical properties with many of these studies being theoretical. One useful photophysical property is the ability to fluoresce with high quantum yields. Natural bases practically do not fluoresce, so being able to design molecules that fluoresce is a goal of practical importance. Many of the modified nucleobases discussed in this review are fluorescent analogues, analogues that have very different fluorescent properties from the natural bases. The studies reviewed here may provide ways to design other analogues with a set of desired properties.

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References

  1. Bag SS, Heemstra JM, Saito Y, Chenoweth DM (2012) Expansion of the genetic alphabet: unnatural nucleobases and their applications. J Nucleic Acids 2012:718582

    Google Scholar 

  2. Callis PR (1983) Electronic states and luminescence of nucleic acid systems. Ann Rev Phys Chem 34:329

    CAS  Google Scholar 

  3. Daniels M, Hauswirth W (1971) Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral aqueous solution at 300 k. Science 171:675

    CAS  Google Scholar 

  4. Daniels M (1976) In: Wang SY (ed) Photochemistry and photobiology of nucleic acids, vol 1. Academic, New York, p 23

    Google Scholar 

  5. Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Ultrafast excited-state dynamics in nucleic acids. Chem Rev 104:1977

    CAS  Google Scholar 

  6. Middleton CT, de La Harpe K, Su C, Law YK, Crespo-Hernandez CE, Kohler B (2009) DNA excited-state dynamics: from single bases to the double helix. Annu Rev Phys Chem 60:217–239

    CAS  Google Scholar 

  7. Sobolewski AL, Domcke W (2006) The chemical physics of the photostability of life. Europhys News 37:20–23

    CAS  Google Scholar 

  8. Shapiro R (1995) The prebiotic role of adenine: a critical analysis. Origins Life Evol Biosph 25:83–98

    CAS  Google Scholar 

  9. Levy M, Miller SL (1998) The stability of the RNA bases: implications for the origin of life. Proc Natl Acad Sci U S A 95:7933–7938

    CAS  Google Scholar 

  10. Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99–123

    CAS  Google Scholar 

  11. Ehrenfreund P, Rasmussen S, Cleaves J, Chen LH (2006) Experimentally tracing the key steps in the origin of life: the aromatic world. Astrobiology 6:490–520

    CAS  Google Scholar 

  12. Limbach PA, Crain PF, McCloskey JA (1994) Summary: the modified nucleosides of RNA. Nucleic Acids Res 22:2183–2196

    CAS  Google Scholar 

  13. Cockell CS, Horneck G (2001) The history of the UV radiation climate of the Earth – theoretical and space-based observations. Photochem Photobiol 73:447–451

    CAS  Google Scholar 

  14. Lakowicz JR (2006) Principles of fluorescence spectroscopy. Springer, New York

    Google Scholar 

  15. Asseline U (2006) Development and applications of fluorescent oligonucleotides. Curr Org Chem 10:491–518

    CAS  Google Scholar 

  16. Rist M, Marino J (2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr Org Chem 6:775–793

    CAS  Google Scholar 

  17. Hall KB (2009) 2-Aminopurine as a probe of RNA conformational transitions. Methods Enzymol 469:269–285

    CAS  Google Scholar 

  18. Hawkins ME, Brand L, Michael LJ (2008) Fluorescent pteridine probes for nucleic acid analysis. Methods Enzymol 450:201

    CAS  Google Scholar 

  19. Sinkeldam RW, Greco NJ, Tor Y (2010) Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 110:2579–2619

    CAS  Google Scholar 

  20. Wilhelmsson LM (2010) Fluorescent nucleic acid base analogues. Q Rev Biophys 43:159–183

    CAS  Google Scholar 

  21. Tanpure AA, Pawar MG, Srivatsan SG (2013) Fluorescent nucleoside analogs: probes for investigating nucleic acid structure and function. Isr J Chem 53:366–378

    CAS  Google Scholar 

  22. Tor Y (2007) Fluorescent nucleoside analogs: synthesis, properties and applications. Tetrahedron 63:3415–3614

    Google Scholar 

  23. Kool ET (2002) Replacing the nucleobases in DNA with designer molecules. Acc Chem Res 35:936

    CAS  Google Scholar 

  24. Wilson JN, Kool ET (2006) Fluorescent DNA base replacements: reporters and sensors for biological systems. Org Biomol Chem 4:4265

    CAS  Google Scholar 

  25. Matray TJ, Kool ET (1999) A specific partner for abasic damage in DNA. Nature 399:704

    CAS  Google Scholar 

  26. Grigorenko NA, Leumann CJ (2009) 2-Phenanthrenyl-DNA: synthesis, pairing, and fluorescence properties. Chem Eur J 15:639

    CAS  Google Scholar 

  27. Hawkins ME (2001) Fluorescent pteridine nucleoside analogs. Cell Biochem Biophys 34:257

    CAS  Google Scholar 

  28. Leonard NJ, Tolman GL (1975) Fluorescent nucleosides and nucleotides. Ann N Y Acad Sci 255:43

    CAS  Google Scholar 

  29. Dierckx A, Miannay F-A, Ben Gaied N, Preus S, Bjorck M, Brown T, Wilhelmsson LM (2012) Quadracyclic adenine: a non-perturbing fluorescent adenine analogue. Chem Eur J 18:5987–5997

    CAS  Google Scholar 

  30. Zhao Y, Knee JL, Baranger AM (2008) Characterization of two adenosine analogs as fluorescence probes in RNA. Bioorg Chem 36:271–277

    CAS  Google Scholar 

  31. Yarkony DR (1998) Conical intersections: diabolical and often misunderstood. Acc Chem Res 31:511–518

    CAS  Google Scholar 

  32. Yarkony DR (1996) Diabolical conical intersections. Rev Mod Phys 68:985–1013

    CAS  Google Scholar 

  33. Yarkony DR (1996) Current issues in nonadiabatic chemistry. J Phys Chem 100:18612–18628

    CAS  Google Scholar 

  34. Yarkony DR (2001) Conical intersections: the new conventional wisdom. J Phys Chem A 105:6277–6293

    CAS  Google Scholar 

  35. Bernardi F, Olivucci M, Robb MA (1990) Predicting forbidden and allowed cycloaddition reactions: potential surface topology and its rationalization. Acc Chem Res 23:405–412

    CAS  Google Scholar 

  36. Bernardi F, Olivucci M, Robb MA (1996) Potential energy surface crossings in organic photochemistry. Chem Soc Rev 25:321–328

    CAS  Google Scholar 

  37. Robb MA, Garavelli M, Olivucci M, Bernardi F (2000) A computational strategy for organic photochemistry. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry, vol 15. Wiley-VCH, New York, pp 87–146

    Google Scholar 

  38. Barckholtz TA, Miller TA (1998) Quantitative insights about molecules exhibiting Jahn-Teller and related effects. Int Rev Phys Chem 17:435–524

    CAS  Google Scholar 

  39. Domcke W, Yarkony DR, Köppel H (2004) Conical intersections. World Scientific, Singapore

    Google Scholar 

  40. Jasper AW, Zhu C, Nangia S, Truhlar DG (2004) Introductory lecture: nonadiabatic effects in chemical dynamics. Faraday Discuss 127:1–22

    CAS  Google Scholar 

  41. Matsika S (2007) Conical intersections in molecular systems. In Lipkowitz KB, Cundari TR (eds) Reviews in computational chemistry, vol 23. Wiley-VCH, New Jersey, pp 83–124

    Google Scholar 

  42. Matsika S, Krause P (2011) Nonadiabatic events and conical intersections. Annu Rev Phys Chem 62:621–643

    CAS  Google Scholar 

  43. von Neumann J, Wigner EP (1929) On the behaviour of eigenvalues in adiabatic processes. Physik Z 30:467–470

    Google Scholar 

  44. Teller E (1937) The crossing of potential surfaces. J Phys Chem 41:109–116

    CAS  Google Scholar 

  45. Koga N, Morokuma K (1985) Determination of the lowest energy point on the crossing seam between two potential surfaces using the energy gradient. Chem Phys Lett 119:371–374

    CAS  Google Scholar 

  46. Farazdel A, Dupuis M (1991) On the determination of the minimum on the crossing seam of two potential energy surfaces. J Comput Chem 12:276–282

    CAS  Google Scholar 

  47. Yarkony DR (1990) On the characterization of regions of avoided surface crossings using an analytic gradient based method. J Chem Phys 92:2457–2463

    CAS  Google Scholar 

  48. Manaa MR, Yarkony DR (1993) On the intersection of two potential energy surfaces of the same symmetry. Systematic characterization using a Lagrange multiplier constrained procedure. J Chem Phys 99:5251–5256

    CAS  Google Scholar 

  49. Anglada JM, Bofill JM (1997) A reduced-restricted-quasi-Newton-Raphson method for locating and optimizing energy crossing points between two potential energy surfaces. J Comput Chem 18:992–1003

    CAS  Google Scholar 

  50. Ragazos IN, Robb MA, Bernardi F, Olivucci M (1992) Optimization and characterization of the lowest energy point on a conical intersection using an MC-SCF Lagrangian. Chem Phys Lett 119:217–223

    Google Scholar 

  51. Bearpark MJ, Robb MA, Schlegel HB (1994) A direct method for the location of the lowest energy point on a potential surface crossing. Chem Phys Lett 223:269–274

    CAS  Google Scholar 

  52. Zilberg S, Hass Y (1999) Molecular photochemistry: a general method for localizing conical intersections using the phase-change rule. Chem Eur J 5:1755–1765

    CAS  Google Scholar 

  53. Ciminelli C, Granucci G, Persico M (2004) The photoisomerization mechanism of azobenzene: a semiclassical simulation of nonadiabatic dynamics. Chem Eur J 10:2327–2341

    CAS  Google Scholar 

  54. De Vico L, Olivucci M, Lindh R (2005) New general tools for constrained geometry optimizations. J Chem Theory Comput 1:1029–1037

    Google Scholar 

  55. Levine BG, Coe JD, Martinez TJ (2008) Optimizing conical intersections without derivative coupling vectors: application to multistate multireference second-order perturbation theory (MS-CASPT2). J Phys Chem B 112:405–413

    CAS  Google Scholar 

  56. Kistler KA, Matsika S (2009) Quantum mechanical studies of the photophysics of DNA and RNA Bases. In Lee T-S, York DM (eds) Challenges and advances in computational chemistry and physics: multi-scale quantum models for biocatalysis: modern techniques and applications, vol 7. Springer, The Netherlands, pp 285–339

    Google Scholar 

  57. Merchán M, Gonzalez-Luque R, Climent T, Serrano-Andrés L, Rodriuguez E, Reguero M, Pelaez D (2006) Unified model for the ultrafast decay of pyrimidine nucleobases. J Phys Chem B 110:26471–26476

    Google Scholar 

  58. Barbatti M, Aquino AJA, Szymczak JJ, Nachtigallova D, Hobza P, Lischka H (2010) Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases. Proc Natl Acad Sci U S A 107:21453–21458

    CAS  Google Scholar 

  59. Ismail N, Blancafort L, Olivucci M, Kohler B, Robb MA (2002) Ultrafast decay of electronically excited singlet cytosine via π, π* to nπ* state switch. J Am Chem Soc 124:6818

    CAS  Google Scholar 

  60. Kistler KA, Matsika S (2007) Radiationless decay mechanism of cytosine: an ab initio study with comparisons to the fluorescent analogue 5-methyl-2-pyrimidinone. J Phys Chem A 111:2650–2661

    CAS  Google Scholar 

  61. Sobolewski AL, Domcke W (2002) On the mechanism of nonradiative decay of DNA bases: ab initio and TDDFT results for the excited states of 9H-adenine. Eur Phys J D 20:369

    CAS  Google Scholar 

  62. Blancafort L, Cohen B, Hare P, Kohler B, Robb M (2005) Singlet excited-state dynamics of 5-fluorocytosine and cytosine: an experimental and computational study. J Phys Chem A 109:4431–4436

    CAS  Google Scholar 

  63. Malone RJ, Miller AM, Kohler B (2003) Singlet excited-state lifetimes of cytosine derivatives measured by femtosecond transient absorption. Photochem Photobiol 77:158–164

    CAS  Google Scholar 

  64. Zgierski MZ, Patchkovskii S, Fujiwara T, Lim EC (2005) On the origin of the ultrafast internal conversion of electronically excited pyrimidine bases. J Phys Chem A 109:9384–9387

    CAS  Google Scholar 

  65. Zgierski MZ, Fujiwara T, Kofron WG, Lim EC (2007) Highly effective quanching of the ultrafast radiationless decay of photoexcited pyrimidine bases by covalent modification: photophysics of 5,6-trimethylenecytosine and 5,6-trimethyleneuracil. Phys Chem Chem Phys 9:3206–3209

    CAS  Google Scholar 

  66. Zgierski MZ, Patchkovskii S, Lim EC (2005) Ab initio study of a biradical radiationless decay channel of the lowest excited electronic state of cytosine and its derivatives. J Chem Phys 123:081101

    Google Scholar 

  67. Zgierski MZ, Patchkovskii S, Fujiwarab T, Lim EC (2007) The role of out-of-plane deformations in subpicosecond internal conversion of photoexcited purine bases: absence of the ultrafast decay channel in propanodeoxyguanosine. Chem Phys Lett 440:145–149

    CAS  Google Scholar 

  68. Zgierski MZ, Patchkovskii S, Lim EC (2007) Biradical radiationless decay channel in adenine and its derivatives. Can J Chem 85:124

    CAS  Google Scholar 

  69. Zgierski MZ, Fujiwara T, Kofron WG, Lim EC (2007) Highly effective quenching of the ultrafast radiationless decay of photoexcited pyrimidine bases by covalent modification: photophysics of 5,6-trimethylenecytosine and 5,6-trimethyleneuracil. Phys Chem Chem Phys 9:3206–3209

    CAS  Google Scholar 

  70. Zgierski MZ, Fujiwara T, Kofron WG, Lim EC (2008) Conical intersections and ultrafast intramolecular excited-state dynamics in nucleic acid bases and electron donoracceptor molecules. Chem Phys Lett 463:289–299

    CAS  Google Scholar 

  71. Ho J-W, Yen H-C, Chou W-K, Weng C-N, Cheng L-H, Shi H-Q, Lai S-H, Cheng P-Y (2011) Disentangling Intrinsic ultrafast excited-state dynamics of cytosine tautomers. J Phys Chem A 115:8406–8418

    CAS  Google Scholar 

  72. Yuan S, Ma J, Zhang W-Y, Shu K-X, Dou Y-S (2012) Semiclassical dynamics simulation and CASSCF calculation for 5-methyl cytosine and cytosine. Acta Phys Chim Sin 28:2803–2808

    CAS  Google Scholar 

  73. Serrano-Andrés L, Merchán M (2009) Are the five natural DNA/RNA base monomers a good choice from natural selection? A photochemical perspective. J Photoch Photobiol C Photochem Rev 10:21–32

    Google Scholar 

  74. Gustavsson T, Banyasz A, Sarkar N, Markovitsi D, Improta R (2008) Assessing solvent effects on the singlet excited state lifetime of uracil derivatives: a femtosecond fluorescence upconversion study in alcohols and D2O. Chem Phys 350:186–192

    CAS  Google Scholar 

  75. Gustavsson T, Sarkar N, Banyasz A, Markovitsi D, Improta R (2007) Solvent effects on the steady-state absorption and fluorescence spectra of uracil, thymine and 5-fluorouracil. Photochem Photobiol 83(3):595–599

    CAS  Google Scholar 

  76. Gustavsson T, Banyasz A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch M, Barone V, Improta R (2006) Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives. J Am Chem Soc 128(2):607–619

    CAS  Google Scholar 

  77. Santoro F, Barone V, Gustavsson T, Improta R (2006) Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: a computational study of 5-fluorouracil and uracil in acetonitrile and water. J Am Chem Soc 128(50):16312–16322

    CAS  Google Scholar 

  78. Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D (2006) Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water. J Phys Chem B 110:12843

    CAS  Google Scholar 

  79. Santoro F, Improta R, Barone V (2009) Three-dimensional diabatic models for the pi pi*– > n pi* excited-state decay of uracil derivatives in solution. Theor Chem Acc 123:273

    CAS  Google Scholar 

  80. Mercier Y, Reguero M (2011) Comparison of the deactivation mechanism of 5-fluorouracil with that of its parent system, uracil: the need of the use of the MS-CASPT2 method. Int J Quantum Chem 111:3405

    CAS  Google Scholar 

  81. Yamazaki S, Taketsugu T (2012) Nonradiative deactivation mechanisms of uracil, thymine, and 5-fluorouracil: a comparative ab initio study. J Phys Chem A 116:491

    CAS  Google Scholar 

  82. Hudock HR, Levine BG, Thompson AL, Satzger H, Townsend D, Gador N, Ullrich S, Stolow A, Martinez TJ (2007) Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine. J Phys Chem A 111:8500–8508

    CAS  Google Scholar 

  83. Gustavsson T, Improta R, Banyasz A, Vaya I, Markovitsi D (2012) The effect of methylation on the excited state dynamics of aminouracils. J Photochem Photobiol A Chem 234:37–43

    CAS  Google Scholar 

  84. Kistler KA, Matsika S (2007) The fluorescence mechanism of 5-methyl-2-pyrimidinone: an ab initio study of a fluorescent pyrimidine analog. Photoch Photob 83:611–624

    CAS  Google Scholar 

  85. Yamazaki S, Sobolewski AL, Domcke W (2009) Photophysics of xanthine: computational study of the radiationless decay mechanisms. Phys Chem Chem Phys 11:10165–10174

    CAS  Google Scholar 

  86. Perun S, Sobolewski AL, Domcke W (2006) Ab initio studies of the photophysics of 2-aminopurine. Mol Phys 104:1113–1121

    CAS  Google Scholar 

  87. Beak P, Fry FSJ, Lee J, Steele F (1975) Equilibration studies. Protomeric equilibria of 2- and 4-hydroxypyridines, 2- and 4-hydroxypyrimidines, 2- and 4-mercaptopyridines, and structurally related compounds in the gas phase. J Am Chem Soc 98:171

    Google Scholar 

  88. Kaluzhny DN, Mikhailov SN, Efimtseva EV, Borisova OF, Florentiev VL, Shchyolkina AK, Jovin TM (2003). Fluorescent 2-pyrimidinone nucleoside in parallel-stranded DNA. Nucleosides Nucleotides and Nucleic Acids 22:1499–1503

    Google Scholar 

  89. Kistler KA, Matsika S (2007) Cytosine in context: a theoretical study of substituent effects on the excitation energies of 2-pyrimidinone derivatives. J Phys Chem A 111:8708–8716

    CAS  Google Scholar 

  90. Kistler KA, Matsika S (2008) Three-state conical intersections in cytosine and pyrimidinone bases. J Chem Phys 128:215102

    Google Scholar 

  91. Krygowski TM, Stepien BT (2005) Sigma- and pi-electron delocalization: focus on substituent effects. Chem Rev 105:34823512

    Google Scholar 

  92. Laland SG, Serck-Hanssen G (1964) Synthesis of pyrimidin-2-one deoxyribosides and their ability to support the growth of the deoxyriboside-requiring organism Lactobacillus acidophilus R26. Biochem J 90:76–81

    CAS  Google Scholar 

  93. Atchity GJ, Xantheas SS, Ruedenberg K (1991) Potential energy surfaces near intersections. J Chem Phys 95:1862

    Google Scholar 

  94. Lobsiger S, Frey H-M, Leutwyler S, Morgan P, Pratt D (2011) S-0 and S-1 state structure, methyl torsional barrier heights, and fast intersystem crossing dynamics of 5-methyl-2-hydroxypyrimidine. J Phys Chem A 115(46):13281–13290

    CAS  Google Scholar 

  95. Ryseck G, Schmierer T, Haiser K, Schreier W, Zinth W, Gilch P (2011) The excited-state decay of 1-methyl-2(1H)-pyrimidinone is an activated process. ChemPhysChem 12:1880

    CAS  Google Scholar 

  96. Nowak MJ, Szczepaniak K, Barski A, Shugar D (1980) Tautomeric equilibria of 2(4)-monooxopyrimidines in the gas-phase, in low-temperature matrices and in solution. J Mol Struct 62:47–69

    CAS  Google Scholar 

  97. Delchev VB, Sobolewski A, Domcke W (2010) Comparison of the non-radiative decay mechanisms of 4-pyrimidinone and uracil: an ab initio study. Phys Chem Chem Phys 11:5007–5015

    Google Scholar 

  98. Vranken H, Smets J, Maest G, Lapinski L, Nowak MJ, Adamowicz L (1994) Infrared-spectra and tautomerism of isocytosine - an ab-initio and matrix-isolation study. Spectrochim Acta A 50:875–889

    Google Scholar 

  99. Shukla M, Leszczynski J (2000) Investigations of the excited-state properties of isocytosine: an ab initio approach. Int J Quantum Chem 77:240–254

    CAS  Google Scholar 

  100. Bakalska RI, Delchev VB (2012) Comparative study of the relaxation mechanisms of the excited states of cytosine and isocytosine. J Mol Model 18:5133–5146

    CAS  Google Scholar 

  101. Hudson RHE, Dambenieks AK, Viirre RD (2004) Fluorescent 7-deazapurine derivatives from 5-iodocytosine via a tandem cross-coupling-annulation reaction with terminal alkynes. Synlett 13:2400–2402

    Google Scholar 

  102. Berry DA, Jung K-Y, Wise DS, Sercel AD, Pearson WH, Mackie H, Randolph JB, Somers RL (2004) Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides. Tetrahedron Lett 45:2457–2461

    CAS  Google Scholar 

  103. Thompson KC, Miyake N (2005) Properties of a new fluorescent cytosine analogue, pyrrolocytosine. J Phys Chem B 109:6012–6019

    CAS  Google Scholar 

  104. Hardman SJO, Botchway SW, Thompson KC (2008) Evidence for a nonbase stacking effect for the environment-sensitive fluorescent base pyrrolocytosine-comparison with 2-aminopurine. Photochem Photobiol 84:1473–1479

    CAS  Google Scholar 

  105. Wojciechowski F, Hudson RHE (2008) Fluorescence and hybridization properties of peptide nucleic acid containing a substituted phenylpyrrolocytosine designed to engage guanine with an additional H-bond. J Am Chem Soc 130:1257412575

    Google Scholar 

  106. Lin K-Y, Jones RJ, Matteucci M (1995) Tricyclic 2′-deoxycytidine analogs: syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J Am Chem Soc 117:38733874

    Google Scholar 

  107. Wilhelmsson LM, Sandin P, Holmén A, Albinsson B, Lincoln P, Nordén B (2003) Photophysical characterization of fluorescent DNA base analogue, tC. J Phys Chem B 107:9094–9101

    CAS  Google Scholar 

  108. Engman KC, Sandin P, Osborne S, Brown T, Billeter M, Lincoln P, Nordén B, Albinsson B, Wilhelmsson LM (2004) DNA adopts normal b-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-vis spectroscopy characterization. Nucleic Acids Res 32:5087–5095

    CAS  Google Scholar 

  109. Sandin P, Brjesson K, Li H, MÃ¥rtensson J, Brown T, Wilhelmsson LM, Albinsson B (2008) Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue. Nucleic Acids Res 36:157

    CAS  Google Scholar 

  110. Börjesson K, Preus S, El-Sagheer AH, Brown T, Albinsson B, Wilhelmsson LM (2009) Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems. J Am Chem Soc 131:4288

    Google Scholar 

  111. Preus S, Borjesson K, Kilsa K, Albinsson B, Wilhelmsson L (2010) Characterization of nucleobase analogue FRET acceptor tC(nitro). J Phys Chem B 114:1050–1056

    CAS  Google Scholar 

  112. Preus S, Kilsa K, Wilhelmsson L, Albinsson B (2010) Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family. Phys Chem Chem Phys 12:8881–8892

    CAS  Google Scholar 

  113. Mburu E, Matsika S (2008) An ab initio study of substituent effects on the excited states of purine derivatives. J Phys Chem A 112:12485–12491

    CAS  Google Scholar 

  114. Cohen B, Hare P, Kohler B (2003) Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism. J Am Chem Soc 125:13594

    CAS  Google Scholar 

  115. Marian CM (2007) The guanine tautomer puzzle: quantum chemical investigation of ground and excited states. J Phys Chem A 111:1545–1553

    CAS  Google Scholar 

  116. Mons M, Piuzzi F, Dimicoli I, Gorb L, Lesczynski J (2006) Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: evidence for the observation of three rare tautomers. J Phys Chem A 110:10921–10924

    CAS  Google Scholar 

  117. Chen H, Li SH (2006) Theoretical study on the excitation energies of six tautomers of guanine: evidence for the assignment of the rare tautomers. J Phys Chem A 110:12360–12362

    CAS  Google Scholar 

  118. Serrano-Andres L, Merchan M, Borin AC (2008) A three-state model for the photophysics of guanine. J Am Chem Soc 130:2473–2484

    CAS  Google Scholar 

  119. Serrano-Andrés L, Merchán M, Borin AC (2006) Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry. Proc Natl Acad Sci U S A 103:8691–8696

    Google Scholar 

  120. Marian CM, Kleinschmidt M, Tatchen J (2008) The photophysics of 7H-adenine: a quantum chemical investigation including spin-orbit effects. Chem Phys 347:346–359

    CAS  Google Scholar 

  121. Serrano-Andres L, Merchan M, Borin AC (2006) A three-state model for the photophysics of adenine. Chem A Eur J 12:6559–6571

    CAS  Google Scholar 

  122. Lang P, Gerez C, Tritsch D, Fontecave M, Biellmann J-F, Burger A (2003) Synthesis of 8-vinyladenosine 50-di- and 50-triphosphate: evaluation of the diphosphate compound on ribonucleotide reductase. Tetrahedron 59:7315–7322

    CAS  Google Scholar 

  123. Gaied NB, Glasser N, Ramalanjaona N, Beltz H, Wolff P, Marquet R, Burger A, Mly Y (2005) 8-Vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2′-deoxyribosyl-2-aminopurine with improved properties. Nucl Acids Res 33:1031–1039

    Google Scholar 

  124. Kenfack CA, Burger A, Mély Y (2006) Excited-state propertes and transitions of fluorescent 8-vinyl adenosine in DNA. J Phys Chem A 110:26327–26336

    CAS  Google Scholar 

  125. Kodali G, Kistler KA, Narayanan M, Matsika S, Stanley RJ (2010) Change in electronic structure upon optical excitation of 8-vinyladenosine: an experimental and theoretical study. J Phys Chem A 114:256–267

    CAS  Google Scholar 

  126. Narayanan M, Kodali G, Singh VR, Velvadapu V, Stanley RJ (2010) Oxidation and reduction potentials of 8-vinyladenosine measured by cyclic voltammetry: implications for photoinduced electron transfer quenching of a fluorescent adenine analog. J Phys Chem A 114:256–267

    Google Scholar 

  127. Nadler A, Strohmeier J, Diederichsen U (2011) 8-Vinyl-2′-deoxyguanosine as a fluorescent 2′-deoxyguanosine mimic for investigating DNA hybridization and topology. Angew Chem Int Ed 50:5392–5396

    CAS  Google Scholar 

  128. Muellar S, Strohmeier J, Diederichsen U (2012) 8-Vinylguanine nucleo amino acid: a fluorescent PNA building block. Org Lett 14(6):1382–1385

    CAS  Google Scholar 

  129. Holzberger B, Strohmeier J, Siegmund V, Diederichsen U, Marx A (2012) Enzymatic synthesis of 8-vinyl- and 8-styryl-2′-deoxyguanosine modified DNA-novel fluorescent molecular probes. Bioorg Med Chem Lett 22(9):3136–3139

    CAS  Google Scholar 

  130. Nir E, Kleinermanns K, Grace L, de Vries MS (2001) On the photochemistry of purine nucleobases. J Phys Chem A 105:5106

    CAS  Google Scholar 

  131. Callahan MP, Crews B, Abo-Riziq A, Grace L, de Vries MS, Gengeliczki Z, Holmes TM, Hill GA (2007) IR-UV double resonance spectroscopy of xanthine. Phys Chem Chem Phys 9:4587–4591

    CAS  Google Scholar 

  132. Nir E, Grace LI, Brauer B, de Vries MS (1999) REMPI spectroscopy of jet-cooled guanine. J Am Chem Soc 121:4896–4897

    CAS  Google Scholar 

  133. Crews B, Abo-Riziq A, Grace LI, Callahan M, Kabelác M, Hobza P, de Vries MS (2005) IR-UV double reonance spectroscopy of guanine-H2O clusters. Phys Chem Chem Phys 7:3015–3020

    CAS  Google Scholar 

  134. Abo-Riziq A, Crews BO, Compagnon I, Oomens J, Meijer G, Helden GV, Kabelác M, Hobza P, de Vries MS (2007) The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine. J Phys Chem A 111:7529–7536

    CAS  Google Scholar 

  135. Ward DC, Reich E, Stryer L (1969) Fluorescence studies of nucleotides and polynucleotides. J Biol Chem 244:1228

    CAS  Google Scholar 

  136. Seefeld KA, Plützer C, Löwenich D, Häber T, Linder R, Kleinermanns K, Tatchen J, Marian CM (2005) Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory. Phys Chem Chem Phys 7:3021–3026

    CAS  Google Scholar 

  137. Feng K, Engler G, Seefeld K, Kleinermanns K (2009) Disperesed fluorescence and delayed ionizaton of jet-cooled 2-aminopurine: relaxation to a dark state causes weak fluorescence. ChemPhysChem 10:886–889

    CAS  Google Scholar 

  138. Lobsiger S, Sinha RK, Trachsel M, Leutwyler S (2011) Low-lying excited states and nonradiative processes of the adenine analogues 7H- and 9H-2-aminopurine. J Chem Phys 134:114307

    Google Scholar 

  139. Perun S, Sobolewski AL, Domcke W (2005) Ab Initio studies on the radiationless decay mechanisms of the lowest excited singlet states of 9H-adenine. J Am Chem Soc 127:6257–6265

    CAS  Google Scholar 

  140. Ludwig V, do Amaral M, da Costa Z, Borin A, Canuto S, Serrano-Andres L (2008) 2-Aminopurine non-radiative decay and emission in aqueous solution: a theoretical study. Chem Phys Lett 463:201–205

    Google Scholar 

  141. Gengeliczki Z, Callahan MP, Svadlenak N, Pongor CI, Sztaray B, Meerts L, Nachtigallova D, Hobza P, Barbatti M, Lischka H, de Vries MS (2010) Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurine. Phys Chem Chem Phys 12:5375–5388

    CAS  Google Scholar 

  142. Barbatti M, Lischka H (2007) Can the nonadiabatic photodynamics of aminopyrimidine be a model for the ultrafast deactivation of adenine? J Phys Chem A 111:2852–2858

    CAS  Google Scholar 

  143. Peon J, Villabona-Monsalve J, Noria R, Matsika S (2012) On the accessibility to conical intersections in purines: hypoxanthine and its singly protonated and deprotonated forms. J Am Chem Soc 134:7820–7829

    Google Scholar 

  144. Chen J, Kohler B (2012) Ultrafast nonradiative decay by hypoxanthine and several methylxanthines in aqueous and acetonitrile solution. Phys Chem Chem Phys 14:10677–10682

    CAS  Google Scholar 

  145. Röttger K, Siewertsen R, Temps F (2012) Ultrafast electronic deactivation dynamics of the rare natural nucleobase hypoxanthine. Chem Phys Lett 536:140146

    Google Scholar 

  146. Guo X, Lan Z, Cao Z (2013) Ab initio insight into ultrafast nonadiabatic decay of hypoxanthine: keto-N7H and keto-N9H tautomers. Phys Chem Chem Phys 15:10777–10782

    CAS  Google Scholar 

  147. Shukla M, Leszczynski J (2003) Electronic spectra, excited-state geometries, and molecular electrostatic potentials of hypoxanthine: a theoretical investigation. J Phys Chem A 107(29):5538–5543

    CAS  Google Scholar 

  148. Shukla M, Leszczynski J (2005) Time-dependent density functional theory (TD-DFT) study of the excited state proton transfer in hypoxanthine. Int J Quantum Chem 105(4):387–395

    CAS  Google Scholar 

  149. Callahan MP, Gengeliczki Z, Svadlenak N, Valdes H, Hobza P, de Vries MS (2008) Non-standard base pairing and stacked structures in methyl xanthine clusters. Phys Chem Chem Phys 10:2819–2826

    CAS  Google Scholar 

  150. Villabona-Monsalve JP, Islas RE, Rodríguez-Córdoba W, Matsika S, Peón J (2013) Ultrafast excited state dynamics of allopurinol, a modified DNA base. J Phys Chem A 117:898–904

    CAS  Google Scholar 

  151. Shin RD, Sinkeldam YT (2011) Emissive RNA alphabet. J Am Chem Soc 133:14912–14915

    CAS  Google Scholar 

  152. Samanta PK, Manna AK, Pati SK (2012) Thieno analogues of RNA nucleosides: a detailed theoretical study. J Phys Chem B 116:7618–7626

    CAS  Google Scholar 

  153. Gedik M, Brown A (2013) Computational study of the excited state properties of modified RNA nucleobases. J Photochem Photobiol A Chem 259:25–32

    CAS  Google Scholar 

  154. Harada Y, Suzuki T, Ichimura T, Xu Y (2007) Triplet formation of 4-thiothymidine and its photosensitization to oxygen studied by time-resolved thermal lensing technique. J Phys Chem B 111:5518–5524

    CAS  Google Scholar 

  155. Kuramochi H, Kobayashi T, Suzuki T, Ichimura T (2010) Excited-state dynamics of 6-aza-2-thiothymine and 2-thiothymine: highly efficient intersystem crossing and singlet oxygen photosensitization. J Phys Chem B 114:8782–8789

    CAS  Google Scholar 

  156. Shukla M, Leszczynski J (2004) Multiconfigurational self-consistent field study of the excited state properties of 4-thiouracil in the gas phase. J Phys Chem A 108:72417246

    Google Scholar 

  157. Shukla M, Leszczynski J (2004) Electronic transitions of thiouracils in the gas phase and in solutions: time-dependent density functional theory (TD-DFT) study. J Phys Chem A 108:10367–10375

    CAS  Google Scholar 

  158. Gedik M (2009) TDDFT study of nucleobase thioanalogues and oxo-derivatives excited states. J Theor Comput Chem 8:71–83

    Google Scholar 

  159. Cui G, Fang WH (2013) State-specific heavy-atom effect on intersystem crossing processes in 2-thiothymine: a potential photodynamic therapy photosensitizer. J Chem Phys 138:044315

    Google Scholar 

  160. Wierzchowski J, Wielgus-Kutrowska B, Shugar D (1996) Fluorescence emission properties of 8-azapurines and their nucleosides, and application to the kinetics of the reverse synthetic reaction of PNP. Biochim Biophys Acta 1290:9–17

    Google Scholar 

  161. Seela IMF, Javelakar AM (2005) Replacement of canonical dna nucleobases by benzotriazole and triazolo[4,5-d]pyrimidine: synthesis, fluorescence and ambiguous base pairing. Helv Chim Acta 88:751–765

    CAS  Google Scholar 

  162. Budowa S, Seela F (2010) 2-Azapurine nucleosides: synthesis, properties, and base pairing of oligonucleotides. Chem Biodivers 7:2145–2190

    Google Scholar 

  163. Kobayashi T, Harada Y, Suzuki T, Ichimura T (2008) Excited state characteristics of 6-azauracil in acetonitrile: drastically different relaxation mechanism from uracil. J Phys Chem A 112:13308–13315

    CAS  Google Scholar 

  164. Kobayashi T, Kuramochi H, Harada Y, Suzuki T, Ichimura T (2009) Intersystem crossing to excited triplet state of aza analogues of nucleic acid bases in acetonitrile. J Phys Chem A 113:12088–12093

    CAS  Google Scholar 

  165. Gobbo JP, Borin AC, Serrano-Andrés L (2011) On the relaxation mechanisms of 6-azauracil. J Phys Chem B 115:6243–6251

    CAS  Google Scholar 

  166. Gobbo JP, Borin AC (2012) On the mechanisms of triplet excited state population in 8-azaadenine. J Phys Chem B 116:14000–14007

    CAS  Google Scholar 

  167. Crespo-Hernandez CE, Cohen B, Kohler B (2005) Base stacking controls excited-state dynamics in A-T DNA. Nature 436:1141–1144

    CAS  Google Scholar 

  168. Crespo-Hernandez CE, de La Harpe K, Kohler B (2008) Ground-state recovery following UV excitation is much slower in G.C-DNA duplexes and hairpins than in mononucleotides. J Am Chem Soc 130:19844–10845

    Google Scholar 

  169. Kwok W-M, Ma C, Phillips DL (2006) Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J Am Chem Soc 128:11894–11905

    CAS  Google Scholar 

  170. Buchvarov I, Wang Q, Raytchev M, Trifonov A, Fiebig T (2007) Electronic energy delocalization and dissipation in single- and double-stranded DNA. Proc Natl Acad Sci U S A 104:4794–4797

    CAS  Google Scholar 

  171. Rachofsky EL, Osman R, Ross JBA (2001) Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. Biochemistry 40:946–956

    CAS  Google Scholar 

  172. Wan C, Fiebig T, Schiemann O, Barton J, Zewail A (2000) Femtosecond direct observation of charge transfer between bases in DNA. Proc Natl Acad Sci U S A 97(26):14052–14055

    CAS  Google Scholar 

  173. Kelley SO, Barton JK (1999) Electron transfer between bases in double helical DNA. Science 283:375

    CAS  Google Scholar 

  174. Fiebig T, Wan C, Zewail A (2002) Femtosecond charge transfer dynamics of a modified DNA base: 2-aminopurine in complexes with nucleotides. Chem Phys Chem 3(9):781–788

    CAS  Google Scholar 

  175. O’Neill MA, Becker H-C, Wan C, Barton JK, Zewail AH (2003) Ultrafast dynamics in DNA-mediated electron transfer: base gating and the role of temperature. Angew Chem Int Ed 42:5896–5900

    Google Scholar 

  176. Larsen O, van Stokkum I, de Weerd F, Vengris M, Aravindakumar C, van Grondelle R, Geacintov N, van Amerongen H (2004) Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA duplexes. Phys Chem Chem Phys 6(1):154–160

    CAS  Google Scholar 

  177. Somsen OJG, Keukens LB, Niels de Keijzer M, van Hoek A, van Amerongen H (2005) Structural heterogeneity in DNA: temperature dependence of 2-aminopurine fluorescence in dinucleotides. Chem Phys Chem 6:1622–1627

    CAS  Google Scholar 

  178. Jean JM, Hall KB (2001) 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc Natl Acad Sci U S A 98:37–41

    CAS  Google Scholar 

  179. Hardman SJO, Thompson KC (2006) Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 45:9145–9155

    CAS  Google Scholar 

  180. Hardman SJO, Thompson KC (2007) The fluorescence transition of 2-aminopurine in double- and single-stranded DNA. Int J Quantum Chem 107:20922099

    Google Scholar 

  181. Liang J, Matsika S (2011) Pathways for fluorescence quenching in 2-aminopurine π-stacked with pyrimidine nucleobases. J Am Chem Soc 133:6799–6808

    CAS  Google Scholar 

  182. Liang J, Matsika S (2012) Pathways for fluorescence quenching in 2-aminopurine pi-stacked with pyrimidine nucleobases (vol 133, pg 6799, 2011). J Am Chem Soc 134(25):10713–10714

    CAS  Google Scholar 

  183. Liang J, Nguyen Q, Matsika S (2013) Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with purine nucleobases. Photochem Photobiol Sci 12:1387–1400

    CAS  Google Scholar 

  184. Jean JM, Hall KB (2002) 2-Aminopurine electronic structure and fluorescence properties in DNA. Biochemistry 41:13152–13161

    CAS  Google Scholar 

  185. Dreuw A, Head-Gordon M (2005) Single-reference ab Initio methods for the calculation of excited states of large molecules. Chem Rev 105:4009–4037

    CAS  Google Scholar 

  186. Dreuw A, Weisman JL, Head-Gordon M (2003) Long-range charge-transfer excited states in time-dependent density functional theory require non-local exchange. J Chem Phys 119:2943

    CAS  Google Scholar 

  187. Lange A, Rohrdanz M, Herbert JM (2008) Charge-transfer excited states in a π-stacked adenine dimer, as predicted using long-range-corrected time-dependent density functional theory. J Phys Chem B 112:6304

    CAS  Google Scholar 

  188. Wang Y, Haze O, Dinnocenzo JP, Farid S, Farid RS, Gould IR (2007) Bonded exciplexes. A new concept in photochemical reactions. J Org Chem 72(18):6970–6981

    CAS  Google Scholar 

  189. Wang Y, Haze O, Dinnocenzo JP, Farid S, Farid RS, Gould IR (2008) Bonded exciplex formation: electronic and stereoelectronic effects. J Phys Chem A 112(50):13088–13094

    CAS  Google Scholar 

  190. Nachtigallova D, Aquino AJA, Horn S, Lischka H (2013) The effect of dimerization on the excited state behavior of methylated xanthine derivatives: a computational study. Photochem Photobiol Sci 12:1496

    CAS  Google Scholar 

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Acknowledgements

Support by NSF under grant CHE-1213614 and DOE under grant DE-FG02-08ER15983 is acknowledged. SM thanks the Alexander von Humboldt Foundation for support during a visit to Germany where part of this chapter was written.

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  1. Spiridoula Matsika Temple University, 1901 N.13th Street, Philadelphia, PA, 19122, USA

    Spiridoula Matsika

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  1. Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany

    Mario Barbatti

  2. Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    Antonio Carlos Borin

  3. Department of Physics and Astronomy, The University of Georgia, Athens, Georgia, USA

    Susanne Ullrich

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Matsika, S. (2014). Modified Nucleobases. In: Barbatti, M., Borin, A., Ullrich, S. (eds) Photoinduced Phenomena in Nucleic Acids I. Topics in Current Chemistry, vol 355. Springer, Cham. https://doi.org/10.1007/128_2014_532

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